Introduction: The Pacific oyster (Crassostrea gigas), one of the major aquaculture shellfish worldwide, has strong environmental adaptability. However, genetic diversity and population structure of the Pacific oysters in Dalian Sea, the major natural and farming area of the species in China, has not been systematically investigated, especially at genome-wide level, limiting the conservation and management of the species. Methods: In this study, whole-genome resequencing of 105 individuals from seven Pacific oyster populations, including five wild and one cultured populations in Dalian and one wild population in Qingdao relatively distant from others, were first performed.Results: A total of 2,363,318 single nucleotide polymorphisms (SNPs) were identified. Based on all these SNPs, similar but relatively low genetic diversity (0.2352~0.2527) was found in the seven populations. The principal component analysis (PCA), phylogenetic and population structure analysis consistently revealed weak differentiation among the seven populations. Frequent migration events were detected among the studied populations by TreeMix, which probably led to a high genetic similarity of these populations. Rapid linkage disequilibrium (LD) decay was observed in the genome of the Pacific oyster. Investigation of genome-wide selection signatures of these populations identified many selected genes involved in the biological processes related to DNA metabolism and stability, shell formation, and environmental stress response, which may be critical for oysters to adapt to the stressful environments.Discussion: This study laid theoretical basis for the subsequent germplasm conservation, management and genetic breeding of the indigenous Pacific oysters, and provided novel insights for the adaptive evolutionary mechanism of oysters.

The bacterial community is an essential component of the aquaculture pond ecosystem, which not only improves and restores the aquaculture environment but also maintains a stable ecological equilibrium with the external environment. Here, Illumina 16S rRNA sequencing was conducted to characterize the bacterial community in the ecosystem of sea cucumber Apostichopus japonicus culture ponds, as well as their correlation with overall community structures. The alpha-diversities of bacterial community among water, sediment, and the gut of A. japonicus were consistent across culture ponds from different areas. Specifically, the richness and diversity of bacterial communities were the highest in sediment, followed by the gut, and the lowest in water. The dominant bacterial community among multiple media was Proteobacteria, which occupies a large proportion of the bacterial community structure, followed by Bacteroidetes and Verrucomicrobia. Highly similar bacterial community structures were present in multiple media among different areas, which provides evidence for deterministic natural evolution. Meanwhile, there was a significant difference (p < 0.05) in the specific bacterial communities across the multiple media. The specific functions of the multiple media in the ecosystem are the main reason for the formation of different bacterial communities. This work demonstrates that bacterial communities are the result of natural evolution within the ecosystem during adaptation to the required environment.

Neptunea cumingii is a carnivorous snail with a very high market value, but it cannot be cultivated on a large scale at present due to the lack of an appropriate artificial feed. In this study, we fed N. cumingii four kinds of diets (Cristaria plicata meat, Chlamys farreri mantle, Mytilus edulis meat, and artificial feed) for 90 days and then measured growth indexes and digestive and immune enzyme indexes. We also subjected liver samples to transcriptome sequencing to detect significant differences among the four groups at the transcriptome level. The survival rate of N. cumingii fed with each type of feed was > 90%. The weight, shell length, shell height, and weight gain of the N. cumingii in the C. plicata meat group were significantly higher than those of the other treatment groups, while the values in the artificial feed group were significantly lower than those of the other treatment groups. The superoxide dismutase, catalase, amylase, protease, and lipase activities were higher in the stomach, intestine, and liver of snails in the C. plicata meat feeding group than in those of the other treatment groups, and they were significantly higher than those of the artificial feed group (p < 0.05); the opposite was true for malondialdehyde content. A total of 3407 differentially expressed genes (DEGs) were found in the M. edulis meat group vs. C. plicata meat group comparison. A total of 3422 DEGs genes were identified in the artificial feed group vs. C. plicata meat group comparison. A total of 3,929 DEGs were found in the C. plicata meat group vs. C. farreri mantle group comparison. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found the DEGs in the liver of N. cumingii fed with the different diets were mainly enriched in the energy metabolism, growth, and immunity pathways. Our results indicated that among the four diets tested, C. plicata meat had the best effect on N. cumingii, and they provided an important reference for identification of suitable diets for the development of N. cumingii artificial breeding.

Animals are not only regulated by their own genes but also influenced by symbiotic bacteria, most of which are colonized in the gut. The gut bacterial community is involved in plenty of physiological processes; therefore, intestinal colonization by commensal microbiota is essential to the health of the host animal. Here, metagenome sequencing of the A. japonicus gut, surrounding water, and feed was performed to explore the structural and functional characteristics of the colonized bacteria in the gut of A. japonicus. Results showed that Bacteroidetes and Proteobacteria were the main dominant phyla of the A. japonicus gut, and Formosa, Vibrio, and Lactobacillus were the dominant genera. There was asymmetry between the A. japonicus gut and its surrounding environment in the bacterial community. In terms of the top 50 abundant genera, those colonized in the gut shared a similarity of 26% with those colonized in the surrounding water and a similarity of 30% with those colonized in the feed. According to KEGG annotation, the dominant metabolic pathways in the gut of A. japonicus were glycan biosynthesis and metabolism, nitrogen metabolism, and cysteine and methionine metabolism. This implies that the gut-colonized bacteria of A. japonicus are influenced by the surrounding water and the feed. In addition, the gut-colonized bacteria might be related to the growth and metabolism of A. japonicus.

The complete mitochondrial (mt) genome of Lunella coronata correensis was determined using genome walking techniques in this study. The total length of the mt genome sequence of L. coronata correensis was 16,551 bp, including 13 protein-coding genes, 23 transfer RNA genes, and 2 ribosomal RNA genes. The overall composition of the mitogenome was estimated to be 33.1% for A, 35.3% for T, 13.7% for C, and 19.9% for G, respectively, indicating that an A + T (68.4%)-rich feature occurs in the L. coronata correensis mitogenome. The phylogenetic relationships of 12 mollusk species were constructed based on the complete mtDNA sequences by the neighbor-joining method using MEGA version 7.0 and DNAMAN version 6.0 software.

To identify the genetic characteristics and local adaptation mechanism of the snail Neptunea cumingii in different sea areas of China, specimens from six coastal areas of the Yellow Sea and Bohai Sea were collected. Simplified genome technology was used to study the population genetic structure and genetic diversity level of N. cumingii and to infer the genetic variation pattern of environmental adaptation of this species. In total, 1992 discrete loci with high quality were obtained used for population genomics analysis. The observed heterozygosity was 0.1551–0.1612, and the expected heterozygosity was 0.1064–0.1117. Nucleotide diversity ranged from 0.1120 to 0.1241, and fixation index values ranged from −0.04683 to −0.02041. A total of 330 discrete loci were screened based on two fixation index values and a method associated with environmental factors. Functional annotation showed that the genes of discrete loci were involved in the three major functions of cell composition, biological process, and molecular function, including growth and development and cell metabolism and catalytic activity. These results suggested that different populations of N. cumingii had loci that may be related to local adaptation. The results of this study helped to clarify the level of genetic diversity and the germplasm genetic background of N. cumingii. They also provided information about the genetic mechanism of environmental adaptation of N. cumingii that can be applied to the restoration and management of N. cumingii resources.